[galaxy-dev] Filter options for type=select based on former selection
Hi all! I am facing a simple problem but can?t find a solution to solve it. Before I start describing my problem here is the code from my tool: conditional name=sReference param name=reference type=select label=Select a reference genome help= option value=mm9_64mm9_64/option option value=hg19hg19/option option value=customcustom (from history, fasta)/option /param when value=mm9_64 param name=ref type=hidden value=7596a73211022433 / /when when value=hg19 param name=ref type=hidden value=f73725d4339c9140 / /when when value=custom param name=ref type=hidden value=b5d0b09143f99c68 / param name=cReference format=fasta type=data label=Select the reference genome / /when /conditional conditional name=sCuffcompare param name=cuffcompare type=boolean truevalue=yes falsevalue=no label=Run Cuffcompare? help= / when value=yes conditional name=sRefannotation param name=refannotation type=select label=Will you select a reference annotation from your history or use a GATC supported one? help= option value=no_refNo reference annotation/option option value=supportedSupported/option option value=historyHistory/option /param when value=supported param name=index type=select label=Select reference annotation help= options from_file=gatc_transcriptome_annotations.loc column name=name index=2 / column name=value index=3 / filter type=sort_by column=2 / filter type=param_value ref=sReference.reference column=0/ validator type=no_options message=No annotations are available for the selected reference genome/ /options /param /when when value=history param name=cAnnotation format=gtf type=data label=Select the reference annotation / /when when value=no_ref / /conditional /when when value=no / /conditional As you might see from the code above I am trying to filter the contents for param name=index type=select label=Select reference annotation help= based on the selected value in param name=reference type=select label=Select a reference genome help= (filter type=param_value ref=sReference.reference column=0/). As soon as I try to load this configuration I get the error KeyError: ?sReference.reference?. So it seems, that the tool cannot access the key sReference.reference. I figured out that the tool can access only the top key from the conditional, i.e. I can use filter type=param_value ref=sReference column=0/ and no error appears while reloading the tools config. But this is not useful because sReference does not contain any value for filtering. Does anybody know how the tool can access variables/keys under a conditonal tag without being within the conditional tag itself? Thanks for any help/hints/advice! Cheers, Sascha ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Filter options for type=select based on former selection
Hi Sascha I don't quite understand your question... $sReference.ref is the variable you are looking for, isn't-it? Regards, Hans On 09/04/2012 11:40 AM, Sascha Kastens wrote: Hi all! I am facing a simple problem but can’t find a solution to solve it. Before I start describing my problem here is the code from my tool: conditional name=sReference param name=reference type=select label=Select a reference genome help= option value=mm9_64mm9_64/option option value=hg19hg19/option option value=customcustom (from history, fasta)/option /param when value=mm9_64 param name=ref type=hidden value=7596a73211022433 / /when when value=hg19 param name=ref type=hidden value=f73725d4339c9140 / /when when value=custom param name=ref type=hidden value=b5d0b09143f99c68 / param name=cReference format=fasta type=data label=Select the reference genome / /when /conditional conditional name=sCuffcompare param name=cuffcompare type=boolean truevalue=yes falsevalue=no label=Run Cuffcompare? help= / when value=yes conditional name=sRefannotation param name=refannotation type=select label=Will you select a reference annotation from your history or use a GATC supported one? help= option value=no_refNo reference annotation/option option value=supportedSupported/option option value=historyHistory/option /param when value=supported param name=index type=select label=Select reference annotation help= options from_file=gatc_transcriptome_annotations.loc column name=name index=2 / column name=value index=3 / filter type=sort_by column=2 / filter type=param_value ref=sReference.reference column=0/ validator type=no_options message=No annotations are available for the selected reference genome/ /options /param /when when value=history param name=cAnnotation format=gtf type=data label=Select the reference annotation / /when when value=no_ref / /conditional /when when value=no / /conditional As you might see from the code above I am trying to filter the contents for param name=index type=select label=Select reference annotation help= based on the selected value in param name=reference type=select label=Select a reference genome help= (filter type=param_value ref=sReference.reference column=0/). As soon as I try to load this configuration I get the error KeyError: ’sReference.reference’. So it seems, that the tool cannot access the key sReference.reference. I figured out that the tool can access only the top key from the conditional, i.e. I can use filter type=param_value ref=sReference column=0/ and no error appears while reloading the tools config. But this is not useful because sReference does not contain any value for filtering. Does anybody know how the tool can access variables/keys under a conditonal tag without being within the conditional tag itself? Thanks for any help/hints/advice! Cheers, Sascha ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Filter options for type=select based on former selection
Hi Hans! I try to clarify my problem: The user selects a reference genome from param name=reference type=select label=Select a reference genome help=. So in my scenario the value for $sReference.reference will be either mm9_64 or hg19. This value is needed to filter the supported reference annotations in case the user wants cuffcompare to be run. That?s why I need filter type=param_value ref=sReference.reference column=0/ I hope this brings some light in my problem ;-) Cheers, Sascha Original Message processed by CONSOLIDATE Subject: Re: [galaxy-dev] Filter options for type=select based on former selection Sent: Dienstag, 4. September 2012 12:56 From: Hans-Rudolf Hotz (h...@fmi.ch) Hi Sascha I don?t quite understand your question... $sReference.ref is the variable you are looking for, isn?t-it? Regards, Hans On 09/04/2012 11:40 AM, Sascha Kastens wrote: Hi all! I am facing a simple problem but can t find a solution to solve it. Before I start describing my problem here is the code from my tool: falsevalue=no label=Run Cuffcompare? help= / help= column=0/ label=Select the reference annotation / As you might see from the code above I am trying to filter the contents for based on the selected value in label=Select a reference genome help= (). As soon as I try to load this configuration I get the error KeyError: sReference.reference . So it seems, that the tool cannot access the key sReference.reference. I figured out that the tool can access only the top key from the conditional, i.e. I can use ref=sReference column=0/ and no error appears while reloading the tools config. But this is not useful because sReference does not contain any value for filtering. Does anybody know how the tool can access variables/keys under a conditonal tag without being within the conditional tag itself? Thanks for any help/hints/advice! Cheers, Sascha ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
